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Born in Barham, Suffolk, Clarke joined Ipswich Town academy as an U7 and signed a scholarship with the club in the summer of 2013. He was included in the main squad for the pre-season in the following year.

In July 2015 Clarke went on a trial at Portsmouth,[6] signing a six-month loan deal with the club on 3 August.[7]

On 2 September 2015, Clarke signed a new two-year contract at Ipswich Town, contracting him to the club until June 2017. His loan deal at Portsmouth was subsequently extended until the end of the season in January 2016.

Clarke signed a permanent three-year deal with Pompey on 1 July 2016, after a swap with Ipswich for Adam Webster was agreed.[8] Despite suffering an injury at the end of the 2015–16 campaign which ruled him out of the opening weeks of the new campaign,[9] he established himself as one of Portsmouth's most reliable performers as they won the 2016–17 League Two title. His partnership with Christian Burgess ensured that Portsmouth conceded the fewest league goals over the course of the season, letting in just 40 goals in 46 matches.

On 14 February 2018, after remaining a regular starter, Clarke extended his contract until 2020.[10]